Microarrays and RNA-Seq identify molecular mechanisms driving the end of nephron production

Abstract

BackgroundThe production of nephrons suddenly ends in mice shortly after birth when the remaining cells of the multi-potent progenitor mesenchyme begin to differentiate into nephrons. We exploited this terminal wave of nephron production using both microarrays and RNA-Seq to serially evaluate gene transcript levels in the progenitors. This strategy allowed us to define the changing gene expression states following induction and the onset of differentiation after birth.ResultsMicroarray and RNA-Seq studies of the progenitors detected a change in the expression profiles of several classes of genes early after birth. One functional class, a class of genes associated with cellular proliferation, was activated. Analysis of proliferation with a nucleotide analog demonstrated in vivo that entry into the S-phase of the cell cycle preceded increases in transcript levels of genetic markers of differentiation. Microarrays and RNA-Seq also detected the onset of expression of markers of differentiation within the population of progenitors prior to detectable Six2 repression. Validation by in situ hybridization demonstrated that the markers were expressed in a subset of Six2 expressing progenitors. Finally, the studies identified a third set of genes that provide indirect evidence of an altered cellular microenvironment of the multi-potential progenitors after birth.ConclusionsThese results demonstrate that Six2 expression is not sufficient to suppress activation of genes associated with growth and differentiation of nephrons. They also better define the sequence of events after induction and suggest mechanisms contributing to the rapid end of nephron production after birth in mice.

p53 enables metabolic fitness and self-renewal of nephron progenitor cells

“…9B). Indeed, the significant decrease in the expression of glycolysis pathway genes that has been reported in nephron progenitors at the end of nephrogenesis emphasizes the involvement of metabolic regulation in cell fate decisions (Brunskill et al, 2011), and whether p53 is involved in these temporal metabolic and cell fate decisions remains to be determined.…”

Coordinated repression of cell cycle genes by KDM5A and E2F4 during differentiation

“…The monocyte/macrophage differentiation system recapitulated the dynamics of transcription factor binding and histone modifications at E2F promoters: coincident to the silencing of cell cycle genes, E2F4/p130 and KDM5A were recruited, and the promoter lost H3K4 methylation. Recent RNAseq experiments, which are more quantitative than microarrays, showed that the cell cycle genes as a group experience the greatest decrease in expression, subsequent to the onset of differentiation (18). Previous genome-wide in silico computational analyses of promoters identified key regulators of human cell cycle-regulated genes, with significant enrichment of the E2F, NRF1, NF-Y, and cyclic AMP-responsive element binding motifs in their promoters (19).…”

Erratum: Stromal–epithelial crosstalk regulates kidney progenitor cell differentiation

“…We hypothesize that Fat4 binds to another factor produced by the progenitors to activate Yap/Taz in the progenitors. The mouse ortholog of Dachsous and Fat3, a paralog of Fat4, are both expressed in the progenitor cells where they could be acting as receptors for stromal Fat4 24,25,31 . It will be interesting to determine whether either of these factors mediates Yap/Taz activity.…”